Based on your posting you have all the family information you need and are only looking to expound on the incident involving Thomas.
California became a State on Sep 9, 1850.Nevada County was created in 1851.The following is my own speculation NOT backed by any factual basis.The article found on his bio identified he left his wife and child for California and was killed in the Grass Valley by Indians.There probably would not have been a death certificate.He was probably buried in an unmarked grave.A County Recorder records documents.There probably was not any documents filed.I would believe you already have the best reference information in the above article.He probably was found, dead, with evidence of Indian activity; or the evidence was there but not his body.Depending on just how long he had been in the area, his "shack" may have been burned.
Your "Best" bet would be in any published books or newspaper articles.
I did go through the historic cemetery listings as presented, his name was not identified.You can note many tombstone photo's, most being made long after this period."IF" he was buried in this location, the funds he carried would have paid for any stone, otherwise a very basic marker, if one at all, would have been placed.There is the remote possibility his remains were shipped back to Illinois, but probably unlikely.
The listing of books owned and the volunteer/owner listing is almost two years old, but Here is a full spread link to the references through the Nevada County GenWeb site: http://cagenweb.com/nevada/http://cagenweb.com/nevada/